From a93a30119d6ed27bc7a9e7954446ed9acaddf9b4 Mon Sep 17 00:00:00 2001
From: Ian Kenney <ianmkenney@users.noreply.github.com>
Date: Fri, 13 Oct 2023 15:36:11 -0700
Subject: [PATCH] Automatic deployment to PyPI on release (#3)

* Use MDAnalysis deployment action
* Updated docs to reflect PyPI installations
---
 .github/workflows/deploy.yaml     | 37 +++++++++++++++++++++++++++++++
 README.md                         | 10 +++++++++
 devtools/conda-envs/test_env.yaml |  4 ++++
 docs/source/getting_started.rst   | 31 ++++++++++++++++++++++++--
 pyproject.toml                    |  9 +++++---
 5 files changed, 86 insertions(+), 5 deletions(-)
 create mode 100644 .github/workflows/deploy.yaml

diff --git a/.github/workflows/deploy.yaml b/.github/workflows/deploy.yaml
new file mode 100644
index 0000000..fb1ee1d
--- /dev/null
+++ b/.github/workflows/deploy.yaml
@@ -0,0 +1,37 @@
+name: Build and upload to PyPi
+
+on:
+  push:
+    tags:
+      - "*"
+  release:
+    types:
+      - published
+
+jobs:
+  pypi_push:
+    environment: deploy
+    if: "github.repository == 'MDAnalysis/PathSimAnalysis'"
+    name: Build, upload and test pure Python wheels
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: testpypi_deploy
+        uses: MDAnalysis/pypi-deployment@main
+        if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
+        with:
+          token: ${{ secrets.TEST_PYPI_API_TOKEN }}
+          test_submission: true
+          tests: true
+          test_deps: 'pytest MDAnalysisTests'
+          package_name: 'pathsimanalysis'
+
+      - name: pypi_deploy
+        uses: MDAnalysis/pypi-deployment@main
+        if: github.event_name == 'release' && github.event.action == 'published'
+        with:
+          token: ${{ secrets.PYPI_API_TOKEN }}
+          package_name: 'pathsimanalysis'
+          tests: false
\ No newline at end of file
diff --git a/README.md b/README.md
index ba46a8b..ee1a7f9 100644
--- a/README.md
+++ b/README.md
@@ -72,6 +72,16 @@ conda deactivate
 
 #### With pip
 
+##### Install from PyPI
+
+The latest release of PathSimAnalysis is available on [PyPI](https://pypi.org/project/pathsimanalysis/) and can be installed with:
+
+```
+pip install pathsimanalysis
+```
+
+##### Install from source
+
 To build the package from source, run:
 
 ```
diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
index 0ed4cd2..520fe92 100644
--- a/devtools/conda-envs/test_env.yaml
+++ b/devtools/conda-envs/test_env.yaml
@@ -9,6 +9,10 @@ dependencies:
 
   # MDAnalysis
   - MDAnalysis
+  - scipy>=1.5.0
+  - matplotlib>=1.5.1
+  - numpy>=1.22.3
+
 
   # Testing
   - MDAnalysisTests
diff --git a/docs/source/getting_started.rst b/docs/source/getting_started.rst
index dfd56bb..0e0fb48 100644
--- a/docs/source/getting_started.rst
+++ b/docs/source/getting_started.rst
@@ -6,10 +6,37 @@ This page details how to get started with PathSimAnalysis.
 Installation
 ------------
 
-PathSimAnalysis is currently only installable from source.
+PyPi
+~~~~
+
+PathSimAnalysis can be installed from PyPI with:
+
+.. code-block:: bash
+
+	pip install pathsimanalysis
+
+If you would like to test your installation, use the `test` optional dependencies and run the tests:
+
+.. code-block:: bash
+
+	pip install "pathsimanalysis[test]"
+	pytest --pyargs pathsimanalysis.tests
+
+From source
+~~~~~~~~~~~
+
+If you want the latest (non-release) version of PathSimAnalysis, you should install the package from source.
 
 .. code-block:: bash
 
 	git clone --depth=1 https://github.com/MDAnalysis/PathSimAnalysis
 	cd PathSimAnalysis
-	pip install .
\ No newline at end of file
+	pip install .
+
+If you want to run tests on your installation, install the `test` dependencies and run the tests:
+
+.. code-block:: bash
+
+	pip install ".[test]"
+	pytest --pyargs pathsimanalysis.tests
+
diff --git a/pyproject.toml b/pyproject.toml
index cdfb6b1..b63f464 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -19,6 +19,9 @@ readme = "README.md"
 requires-python = ">=3.9"
 dependencies = [
     "MDAnalysis>=2.0.0",
+    "scipy>=1.5.0",
+    "matplotlib>=1.5.1",
+    "numpy>=1.22.3",
 ]
 keywords = [
     "molecular simulations",
@@ -39,9 +42,9 @@ doc = [
     "sphinx_rtd_theme",
 ]
 
-# [project.urls]
-# source = "https://github.com/MDAnalysis/pathsimanalysis"
-# documentation = "https://pathsimanalysis.readthedocs.io"
+[project.urls]
+source = "https://github.com/MDAnalysis/pathsimanalysis"
+documentation = "https://mdanalysis.org/PathSimAnalysis"
 
 [tool.pytest.ini_options]
 minversion = "6.0"